FMO DATABASE

FMODB ID: G52V1

Calculation Name: 2GYP-A-Xray372

Preferred Name:

Target Type:

Ligand Name: norleucine

ligand 3-letter code: NLE

PDB ID: 2GYP

Chain ID: A

ChEMBL ID:

UniProt ID: P20823

Base Structure: X-ray

Registration Date: 2023-09-23

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	33
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-105198.295309
FMO2-HF: Nuclear repulsion	93038.990713
FMO2-HF: Total energy	-12159.304595
FMO2-MP2: Total energy	-12195.811606

3D Structure

Snapshot

Ligand structure

Ligand Interaction

Ligand binding energy

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
N/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(A:1:NLE)

Summations of interaction energy for fragment #1(A:1:NLE)

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
-0.254	-0.741	0.038	1.504	-1.055	0.003

Interaction energy analysis for fragmet #1(A:1:NLE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.007 / q_NPA : -0.008

Distance from base fragment(s) [Å]

Dist

Interaction energy by IFIE and PIEDA
[kcal/mol]

| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >

Fragment charge [e]

FCHARGE q_Mulliken
q_NPA q(I=>J)

Residue

Res # RES

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Graph Options

X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

frag_NumFragment number.	ChainChain species.	Res #Residue number.	RES3-letter code of amino acid residue, ligand and solvent molecule.	FCHARGEFormal charge [e].	q_MullikenFragment charge evaluated by Mulliken charge [e].	q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e].	DISTDistance from Ligand [Å].	TotalIFIE at MP2 level [kcal/mol].	ESElectro static interaction energy by PIEDA [kcal/mol].	EXExchange-repulsion energy by PIEDA [kcal/mol].	CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol].	DI(MP2)Dispersion energy by PIEDA [kcal/mol].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	3	SER	0	0.019	0.014	2.893	2.408	1.796	0.039	1.514	-0.941	0.003
4	A	4	LYS	1	1.047	1.002	5.968	-2.357	-2.357	0.000	0.000	0.000	0.000
5	A	5	LEU	0	-0.002	0.015	7.999	-0.146	-0.146	0.000	0.000	0.000	0.000
6	A	6	SER	0	0.031	0.006	6.655	-0.031	-0.031	0.000	0.000	0.000	0.000
7	A	7	GLN	0	-0.010	0.002	4.294	-0.174	-0.049	-0.001	-0.010	-0.114	0.000
8	A	8	LEU	0	0.036	0.017	8.304	-0.047	-0.047	0.000	0.000	0.000	0.000
9	A	9	GLN	0	0.013	-0.007	11.613	-0.069	-0.069	0.000	0.000	0.000	0.000
10	A	10	THR	0	-0.010	-0.003	10.157	-0.037	-0.037	0.000	0.000	0.000	0.000
11	A	11	GLU	-1	-0.952	-0.968	10.274	0.254	0.254	0.000	0.000	0.000	0.000
12	A	12	LEU	0	-0.020	-0.023	13.416	-0.010	-0.010	0.000	0.000	0.000	0.000
13	A	13	LEU	0	-0.005	0.011	16.078	-0.011	-0.011	0.000	0.000	0.000	0.000
14	A	14	ALA	0	0.000	0.000	16.161	-0.008	-0.008	0.000	0.000	0.000	0.000
15	A	15	ALA	0	0.029	0.006	17.544	-0.003	-0.003	0.000	0.000	0.000	0.000
16	A	16	LEU	0	-0.007	0.002	19.390	-0.003	-0.003	0.000	0.000	0.000	0.000
17	A	17	LEU	0	-0.019	-0.017	19.789	-0.004	-0.004	0.000	0.000	0.000	0.000
18	A	18	GLU	-1	-0.979	-0.972	21.397	0.008	0.008	0.000	0.000	0.000	0.000
19	A	19	SER	0	-0.101	-0.043	23.356	0.001	0.001	0.000	0.000	0.000	0.000
20	A	20	DAL	0	0.014	-0.006	25.465	0.000	0.000	0.000	0.000	0.000	0.000
21	A	21	LEU	0	-0.061	-0.016	23.521	-0.002	-0.002	0.000	0.000	0.000	0.000
22	A	22	SER	0	0.000	0.005	26.939	-0.006	-0.006	0.000	0.000	0.000	0.000
23	A	23	LYS	1	0.943	0.922	27.902	0.014	0.014	0.000	0.000	0.000	0.000
24	A	24	GLU	-1	-0.828	-0.897	28.849	-0.012	-0.012	0.000	0.000	0.000	0.000
25	A	25	ALA	0	0.016	0.015	27.664	-0.001	-0.001	0.000	0.000	0.000	0.000
26	A	26	LEU	0	0.015	0.012	22.440	0.000	0.000	0.000	0.000	0.000	0.000
27	A	27	ILE	0	-0.038	-0.023	25.631	-0.005	-0.005	0.000	0.000	0.000	0.000
28	A	28	GLN	0	-0.052	-0.023	28.216	-0.004	-0.004	0.000	0.000	0.000	0.000
29	A	29	ALA	0	0.026	0.009	23.406	0.000	0.000	0.000	0.000	0.000	0.000
30	A	30	LEU	0	-0.015	-0.011	22.371	-0.004	-0.004	0.000	0.000	0.000	0.000
31	A	31	GLY	0	0.009	-0.006	24.804	-0.004	-0.004	0.000	0.000	0.000	0.000
32	A	32	GLU	-1	-1.024	-0.985	24.853	0.001	0.001	0.000	0.000	0.000	0.000
33	A	33	TRP	0	-0.100	-0.038	19.209	-0.002	-0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:1:NLE)